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Mol Biochem > Exam 5 > Flashcards

Exam 5 Flashcards

1
Q

tertiary protein structure

A

formation of domains

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2
Q

when does protein folding assistance beginning

A

as soon as peptide emerges

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3
Q

denturants

A

detergents (SDS), chaotropic slats (NaSCN, NaClO4), high temp, Urea, guanidine HCl

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4
Q

Anfinsen’s experiment

A

reduce (BME) then denature (8M Urea) RNaseA (4 S-S). dialysis (remove urea). Oxidize back to S-S. All correct S-S. Swap dialysis and oxidation steps. Random S-S.

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5
Q

lead to protein aggregation (3)

A

hydrophobic region exposed. Very high concentration. hydrophobic regions of monomers binding one another.

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6
Q

Alzheimers protein folding

A

alphabeta protein Beta sheets adhere and form long fibrils

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7
Q

e. coli chaperone

A

DnaK (Hsp70 analog), GroES-GroEL (Hsp 60)

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8
Q

eukaryote chaperone

A

Hsp 70, Hsp90

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9
Q

Hsp70 function

A

bind hydrophobic regions. uses ATP to prevent misfolding. allows time for productive folding

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10
Q

nascent protein 1st met by ? as it leaves ribosome. name pro and euk. Transfers to Hsp70 if needed.

A

TF (pro) , NAC (euk)

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11
Q

three protein folding pathways

A

chaperone independent. Hsp70 assisted. Hsp70 + chaperonin

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12
Q

Dnak (Hsp70 homolog) regions

A

N t-term ATP binding. C-term peptide binding

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13
Q

Hsp70 (DnaK) mechanism

A

DnaJ delivers unfolded or partially folded peptide to DnaK-ATP. Hydrolysis of ATP prevents RAPID folding. GrpE replaces ADP with ATP and partially folded peptide dissociates. Peptide may finish folding independently OR require another cycle OR require GroEL (chaperonin)

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14
Q

GroEL structure/function

A

aka Anfinsens cage. hydrophobic inner regions interact with substrate. Recruits GroES cap. 7 ATP binding sites in central and lower GroEL cavity

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15
Q

GroEl-GroES mechanism

A

peptide binds hydrophobic region in GroES central cavity. 7 ATP and GroES cap bind GroEL central cavity. ATP hydrolzyed over 15 seconds. 7 more ATP bind lower GroEL cavity. ADP and GroES dissociate. folded peptide dissociates.

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16
Q

proteins are delivered to cellular compartments by ?

A

translocation

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17
Q

characteristics of translocated prokarotic proteins

A

preproteins with N-terminal leader sequence

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18
Q

eukaryote synthesis of secretory and membrane proteins coupled to translocation across ?

A

ER membrane

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19
Q

participate in secretory protein translocation

A

SRP (signal recognition particles), SR (signal receptors), and translocons

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20
Q

modifies and sorts secretory and membrane proteins

A

golgi

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21
Q

golgi function for secretory and membrane proteins

A

modifies and sorts

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22
Q

prokaryote N-term leader sequence characteristics

A

total about 26 residues. far N-term (basic residues), central N-term (hydrophobic), C-term of N-term (nonhelical). Also a cleavage site

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23
Q

Unique roll of Hsp90

A

functions on regulated “client proteins” to function. (ie. tyrosine kinases, telomerases) Assists binding. uses ATP

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24
Q

SecB mediated transloaction

A

SecB binds protein to be translocated. binds SecA/SecYEG on membrane. ATP binds and SecB dissociates. ATP hydrolysis drives protein threading through membrane

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25
Q

nuclear peptide targeting sequences

A

positively charged regions (lysine)

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26
Q

ER peptide targeting sequence

A

hydrophobic region

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27
Q

peroxisome targetting sequence

A

-SKL-

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28
Q

secretory protein translocation into ER

A

signal sequence emerges from ribosome. SRP binds and arrests translation. docks ribosome on ER receptor. GTP dissociates SRP and translation resumes through translocon on ER membrane. signal peptidase in ER lumen cleaves signal sequence. BIP (Hsp70) assists folding. SRP hydrolyzes GTP and is recycled. signal is degraded.

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29
Q

fate of ER synthesized proteins

A

secretion, membrane, lysosome

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30
Q

signal recognition particle domains

A

Alu domain (contains 5’ and 3’ ends, translation termination), S domain (signal recognition and ER targeting)

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31
Q

how does SRP Alu domain cause translation arrest

A

competes with elongation factors

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32
Q

eukaryotic ER translocon components

A

docking receptor (composed of Sec61 and TRAM), SP (signal peptidase), OST (adds carbohydrate to peptide)

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33
Q

major modification by golgi and ER

A

glycosylation by enzymes on luminal membrane. post golgi localization is often based on glycosylation

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34
Q

direction of flow through golgi

A

cis to trans. post golgi localization is often based on glycosylation

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35
Q

CFTR

A

cystic fibrosis transmembrane conductance regulator. epithelial Cl- channel. Regulates H2O secretion

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36
Q

deltaF508 effect on CFTR

A

prevents proper trafficking to golgi. Does not lose Cl- channel activity. functions normally if forced onto surface

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37
Q

mutation of CFTR that prevents proper trafficking to golgi

A

deltaF508. functions normally if forced onto surface of golgi

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38
Q

mitochondrial translocon

A

multiple translocons depending on destination. All interact with TOM (outer MM translocon). SAM for outer membrane. Tim22 or 23 for inner membrane or matrix respectively.

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39
Q

nuclear localization signal targets ?

A

importin alpha/beta complex

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40
Q

nuclear translocation

A

peotein binds imortin alpha/beta. movement through nuclear pore complex mediated by RanGTPase. cargo dissociates from beta then alpha. beta and alpha shuttled back to cytosol

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41
Q

protein modifications that generally occur cotranslationally

A

glycosylation, acylation

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42
Q

modifications that generally occur post-translationally

A

proteolytic cleavage, phosphorylation, methylation, sulfation

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43
Q

most common post translational modification

A

proteolytic cleavage

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44
Q

prenylation

A

addition of isoprene lipids (unsaturated lipid)

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45
Q

purpose of glycosylation

A

increased solubility. assist folding. localization. extracellular recognition,

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46
Q

o-linked glycosylation

A

glycosylation of OH groups of Serine or threonine

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47
Q

where does glyosylation of OH groupos of serine or threonine (o-linked) occur?

A

exclusively Golgi

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48
Q

N-linked glycosylation occurs where?

A

starts in ER, continues in golgi

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49
Q

N-linked glycosylation on ? residues

A

asparagine

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50
Q

o-linked glycosylation target sequence

A

no target sequence (:

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51
Q

n-linked glycosylation target sequence

A

-NX(S/T)- X is any but proline

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52
Q

n-linked pentasaccharide core

A

two n-acetylglucosamine and three mannose

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53
Q

dolichol phosphate function

A

first recipient of glycosyl residues destined for protein. located in ER membrane. oligosaccharide destined for attachment to Asn

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54
Q

enzyme that adds sugar to dolichol phosphate

A

glycosylaminotransferases

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55
Q

blocks initial linkage of sugar to dolichol phosphate. how?

A

tunicamycin. mimics UDP-GlcNAc. leads to UPR (unfolded protein response)

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56
Q

dolichol phosphate glycosylation pathway

A

glycosyltransferases add two GlcNAc core to cytosolic side of dolichol. Add 5 mannose. Flips oligosaccharide to ER lumen. Further glucose and mannose transferred from lumen dolichol. oligosaccharyl transferase transfers saccharide from dolichol to protein.

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57
Q

tunicamycin

A

mimics UDP-GlcNAc. blocks assembly of pentasaccharide core. lead to UPR (unfolded protein response)

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58
Q

unfolded protein response (UPR)

A

activate PERK kinase. phosphorylates/inhibits eIF2/protein synthesis

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59
Q

proteins destined for lysosome are marked with ?

A

m6P. mannose 6-phosphate

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60
Q

marks proteins with m6P (for lysosome localization)

A

N-acetylglucosamine transferase.. GlcNAc-transferase

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61
Q

I cell disease

A

caused by inclusion bodies from inability to target proteins to lysosome with m6P label

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62
Q

prenylation consensus sequence

A

-CAAX A is aliphatic, X determines prenylation type

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63
Q

two types of prenylation and consensus sequence

A

Ala, Met, Ser (farnesyl), Leu (geranylgeranyl)

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64
Q

function of prenylation

A

anchors to membrane. signal transduction

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65
Q

farnesyl linkage is to ?. enzyme? occurs where?

A

cysteine thiol. farnesyl protein transferase. in cytosol

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66
Q

fate of prenyl consensus sequence

A

proteolysis of AAX in ER. carboxymethylation of C

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67
Q

H-ras and N-ras fate after prenylation

A

also palmitoylated in ER

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68
Q

HOT target for treatment of Ras mediated cancers

A

farnesyl protein transferase

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69
Q

myristoylation consensus sequence

A

amino terminal.. (M)GXXX(S/T)

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70
Q

myristoylation general mechanism

A

occurs cotranslationally. myristic acid activated by CoA attachment. linkage through amide with glycine

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71
Q

myristoylated proteins

A

often found in cytoplasm or membranes. involved in signal transduction

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72
Q

palmitoylation consensus

A

(M)(X_1-9)C. but not really known

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73
Q

palmitoylation general mechanism

A

reversible ester linked acylation through cysteine

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74
Q

palmitoylation function

A

anchors to membrane. signal transduction

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75
Q

prokaryotic proteins are degraded by ___ or __

A

proteasomes or the HtrA protease

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76
Q

eukaryotic proteins are degraded by

A

proteasomes, HtrA protease or lysosomes

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77
Q

measure protein half life

A

pulse chase. pulse 35SMet for various amounts of time. . to other samples, chase with Met. . PAGE autoradiography

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78
Q

characteristics of unstable protein in pulse chase

A

fast 35SMet incorporaton. fast disappearance

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79
Q

membrane bound organelle disposal site

A

lysosome

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80
Q

lysosomes contain ? for breakdown. how maintained?

A

acid hydrolases. uses H+-ATPase pump

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81
Q

degrade ~85% of intracellular protein

A

26S proteasome in euk. ClpAP in prok

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82
Q

26S proteasome structure

A

20S core19S caps select for ubiquitinated proteins (15 different proteins, 6 ATPases)

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83
Q

26S proteasome 20S core

A

4 rings of 7 subunits (2 alpha rings and 2 beta rings). 2 beta rings make up central chamber. each alpha ring makes up antechamber.

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84
Q

ClpAP function, structure

A

prokaryotic proteasome. ClpA ATP dependent caps. ClpP protease core

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85
Q

ubiquitin linked to ? on protein

A

lysine or alpha-NH2

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86
Q

ubiquitin bonds

A

protein linked to C-term Gly. adjacent ubiquitin linked between c-term gly and a lysine via isopeptide bond

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87
Q

cleaves isopeptide bond between ubiquitin monomers

A

isopeptidase. allows recycling

88
Q

ubiquitin recycling general mechanism

A

E1 binds free Ub. Transfers to E2. E3 attaches to target protein via amide bond.

89
Q

E1 binding Ub mechanism

A

Ub conjugated to Acyl-AMP via ATP hydrolysis. transferred to E1. form shigh energy thioester.

90
Q

E3 Ub mechanism

A

E3 ligase binds protein noncovalently and transfers Ub covalently from E2. Forms isopeptide bond. There are many different E3 ligases that seek different proteins

91
Q

half life of many proteins depends on this sequence

A

n-terminal sequence

92
Q

destabilizing AA of N-term sequence that signal breakdown in prok and euk

A

FLY WRK

93
Q

destabilizing AA of N-term sequence that signal breakdown in EUK

A

HATS

94
Q

Effect of Asp or Glu on N-term

A

indirect destabilizing. Arg-tRNA transferase adds Arg that signals breakdown

95
Q

Effect of Asn or Gln on N-term

A

Converted to Asp or Glu thentargetted for Arg addition for breakdown

96
Q

Arg-tRNA transferase adds Arg that signals breakdown to these AA

A

Asp or Glu. Acidic

97
Q

protein degradation sequence that does not involve N-rule

A

PEST sequence. any order. ubiquination by different set of enzymes

98
Q

enzymes that ubiquinate PEST

A

Ubc1,4,5

99
Q

HtrA dual function

A

chaperone at low temp, proteasome at high temp

100
Q

HtrA catalytic triad

A

Asp-His-Ser

101
Q

HtrA structure.

A

dimer of trimers. PDZ substrate recognition domains reach out. serine protease core.

102
Q

caspases

A

cys+asp-ases. apoptosis. cleaves after Asp

103
Q

metalloproteases

A

Zn requiring endopeptidase. Allow cells to invade be cleaving ECM proteins

104
Q

viral proteinases

A

cleave viral polyprotein precursors. viral encoded. catalytic metal involved. site specific endopeptidase

105
Q

induction

A

increased expression of genes in response to metabolite

106
Q

activator

A

protein that binds operator to activate

107
Q

inducer

A

small molecule that activates gene expression by binding repressor

108
Q

constitutive gene

A

gene is always on at fixed rate

109
Q

operon characteristics

A

genes involved in same pathway. identical transcription regulation. different translation regulation

110
Q

ribosomal protein operons

A

operator is in mRNA

111
Q

adaptation

A

change in expression in response to environmental change. small metabolite acts as inducer. decreases repressor affinity for DNA

112
Q

promoters in lac operon

A

Pi for LacI (repressor), Po for Laz Z Y and A

113
Q

Po operator. regulation?

A

LacO. LacI represses.

114
Q

lac operator acronym

A

PIPOZYA. promoter-LacI-promoter-operator-lacZ-lacY-lacA

115
Q

lac operon induction

A

allolactose acts as inducer and binds lacI (repressor)

116
Q

uninduced vs induced lac operon protein levels

A

10 vs 50,000 copies of beta galactosidase and permease

117
Q

common chemical analog of allolactose

A

IPTG

118
Q

lac operator characteristics

A

three binding sites O1, O2 and O3. O1 is high affinity. Each are palindromic

119
Q

Lac I structure and operator binding

A

dimer of dimers. each dimer binds different operator. interaction is helix-turn-helix

120
Q

e. coli grown in? (glucose and lactose conc)

A

0.2 mg/ml glucose. 4 mg/ml lactose

121
Q

why is beta-galactosidase gene not turned on until glucose is exhausted?

A

low glucose increases cAMP conc. activates CAP activator of Po

122
Q

activation and derepression of lac operon

A

activation (CAP binding), derepression (induced lacI)

123
Q

CAP activation of lac operon

A

as glucose is depleted, cAMP increases. binds CAP. CAP binds Po and recruits RNAP.

124
Q

CAP global function

A

activator of alternative energy sources. lactose, galactose, arabinose…

125
Q

CAP effect on DNA structure

A

introduces bend. protein side chan and DNA phosphate interaction

126
Q

ara operon

A

turned on when arabinose is primary carbon source

127
Q

turned on when arabinose is primary carbon source

A

ara operator

128
Q

genes in the arabinose operator

A

B and A and D. araBAD

129
Q

ara operon responds to ? and ?

A

CAP and araC

130
Q

araC regulation of ara operon

A

araC gene makes araC. araC dimer forms at low arabinose and causes DNA looping over long distance upstream of ara operator. at high arabinose, araC binds CAP (no loop)

131
Q

Trp operon encodes ?

A

leader sequence and 5 proteins involved in Trp synthesis

132
Q

Trp repressor regulates ?

A

Trp operon AND trpR and aroH operons (autogenous)

133
Q

attenuation of Trp operon requires?

A

alternative stem-loops. requires link between transcription and translation (prok). Consecutive Trp codons in mRNA leader

134
Q

Trp operon attenuation at low Trp

A

slow ribosome (resulting from low Trp availability) allows base pairing between sequence 2 and 3. ribosome pausing is sequence 1 inhibits formation of terminator stem loop

135
Q

Trp operon attenuation at high Trp

A

base pairing between sequence 3 and 4. ribosome translates through sequence 1 and 2. 3-4 stem loop inhibits RNAP. early transcription termination. fewer Trp enzymes

136
Q

negative control induction

A

coinducer inactivates repressor

137
Q

positive control induction

A

coinducer activates inducer

138
Q

negative control repression

A

corepressor activates repressor

139
Q

positive control repression

A

corepressor inactivates inducer

140
Q

3 modes of transcription regulation

A

chromatin remodeling, gene arrangement, activation/repression

141
Q

3 modes or translation regulation

A

alternative splicing, mRNA stability, translational control

142
Q

eukaryote transcript processing in nucleus

A

5’ cap (m7GpppG), 3’ cleavage and polyadenylation, introns spliced

143
Q

7 regulatory sites in eukaryote gene expression

A

chromatin, transcription control, RNA transport, RNA stability, translation control, protein processing

144
Q

histone acetylation effect. enzymes

A

loosen nucleosome structure. HAT (acetylation) and HDAC (deacetylation)

145
Q

heritable epigentic modification

A

histone modification as cellular memory

146
Q

H3 Lys4 trimethylation effect on histone

A

gene activation

147
Q

H3 Lys9 methylation effect on histone

A

gene repression

148
Q

coinducer and corepressor effects on chromatin

A

coinducer or corepressor binds TF and has HAT or HDAC activity

149
Q

CpG islands

A

regions of cysteine prone to methylation. occur near promoters. proteins bind that maintain inactive state

150
Q

heterochromatin characteristics

A

DNA is methylated. histone tails not acetylated. histone tails methylated.

151
Q

euchromatin characteristics

A

DNA not methylated, histone tails acetylated.

152
Q

does histone tail acetylation expose DNA for transcription

A

not directly. chromatin remodeling complex causes ATP dependent conformational change

153
Q

TATA box transcription factor

A

TBP

154
Q

GC box transcription factor

A

SP1 (specificity protein)

155
Q

helix-turn-helix DNA binding

A

c-term helix fits into major groove, N-term stabilizes C term

156
Q

Zn finger motifs

A

C2H2 (form beta strand and alpha helix) or Cx (1 st helix dna binding, 2nd packs against first)

157
Q

helix-turn-helix example

A

E. coli CAP, lacI

158
Q

Zn finger example

A

TFIIIA

159
Q

leucine zipper structure

A

28 AA w/ leucine every 7. y shaped dimer. arms bind DNA. stem holds together. homodimer recognizes symmetric site. heterodimer recognizes asymmetric.

160
Q

Leu zipper example

A

Fos

161
Q

activation of transcription by signal transduction example

A

Jak stat pathway response to interferons

162
Q

PEPCK is stimulated for?

A

gluconeogenesis

163
Q

clone DNA procedure

A

restriction endonuclease of DNA to be cloned and of plasmid. ligate. transform bacterial cell. select sells that contain plasmid

164
Q

bioinformatics definition

A

detailed view of expression of all genes in any situation

165
Q

DNA microarrays

A

determine individual identity of every mRNA in cell. quantify by extent of probe hybridization. synthesized DNA with unique sequences. fluorescent probe hybridizes. different tag for each population.

166
Q

RNA deep sequencing

A

sequence (short stretches) each mRNA multiple times. quantify number of times found (abundance). determine isoform and type differences in mRNA

167
Q

G1 phase

A

grow in size, catabolize nutrients, synthesize proteins,

168
Q

S phase

A

replicate DNA

169
Q

G2 phase

A

check and segregate cytoplasmic and nuclear contents

170
Q

M phase

A

localize contents and divide

171
Q

G0 phase

A

cells are still metabolizing but not replicating

172
Q

cyclins degraded by

A

28S proteasome

173
Q

cyclin D regulates __

A

G1/S transition

174
Q

cyclin A regulates ___

A

S/G2 transition

175
Q

cyclin B regulates ___

A

G2/M transition

176
Q

CKIs

A

Cdk inhibitors

177
Q

E2F function

A

induces proliferative genes

178
Q

Rb function

A

tumor suppressor that binds E2F. Cells in G0 and G1 arrest

179
Q

phosphorylate to inactive Rb

A

CyclinD/Cdk

180
Q

epigenetic

A

stable change that alters DNA expression

181
Q

angiogenesis

A

formation of new blood cells

182
Q

formation of new blood cells

A

angiogenesis

183
Q

stable change that alters DNA expression

A

epigenetic

184
Q

p53 function

A

halts cell cycle when DNA is damaged. activates p21 gene and GADD45

185
Q

p21 gene

A

cyclin/cdk inhibitor

186
Q

GADD45 function

A

demethylation to inhibit growth

187
Q

p53 expression in tumors

A

mutated in 50% of tumors

188
Q

EGF receptor as an oncoprotein

A

epidermal growth factor. truncation makes constitutively active. referred to as ErbB protein. gene is amplified in 25% of breast cancers

189
Q

multiple proto-oncogenes in ras pathway

A

ras, raf, fos, jun, myc

190
Q

neurofibromatosis is due to ?. how?

A

Ras misregulation. NF-1 activates Ras innate GTPase activity. Ras-GDP no longer signals to Raf. mutations in NF-1 allows Ras-GTP to persist

191
Q

overexpression of EIF4E or EIF4G

A

transformation and tumor formation

192
Q

tamoxifen

A

antagonist of estrogen receptor

193
Q

ER(+)

A

rely on estrogen for continued growth

194
Q

means of circumventing apoptosis

A

mutate p53. upregulate Bcl2 (antiapoptotic). destroy capsase activity

195
Q

release of ? assembles apoptosome

A

cytochrome C

196
Q

Bcl-2 location and function

A

outer mitochondrial membrane protein

197
Q

apoptosome function

A

releases caspases for apoptosis

198
Q

extrinsic apoptosis signal

A

T-cell mediated

199
Q

intrinsic apoptosis signal

A

GF depletion, irradiation

200
Q

initiator caspases

A

8 and 9

201
Q

executioner caspases

A

3, 6, and 7

202
Q

Apaf1

A

inhibited by Bcl2. makes caspase 9. contains IRES. feedback loop

203
Q

what was the conclusion of anfinsens experiment

A

all necessary information to determine 3D fold is in primary sequence

204
Q

mitochondraa localization signal

A

amphipathic helix. positive charge on one side

205
Q

nuclear localization signal

A

positively charged

206
Q

SRP composition

A

ribonucleoprotein. 7sRNA (300nt) + 6 SRP proteins

207
Q

SRP translation arrest mechanism

A

signal peptide binds SRP54. forms a kink involving srp68. Alu rotates to contact EFS (elongating factor binding site). Alu competes with EF. SRP stretches from peptide exit to the EFS.

208
Q

26S proteasome 19S cap composition

A

15+ dif proteins, 6 ATPases, isopeptidase

209
Q

where are 26S proteasomes located

A

nucleus and cytoplasm

210
Q

step in ubiquitination that requires ATP

A

attachment of AMP to Ub C-term gly

211
Q

HtrA catalytic triad

A

DHS

212
Q

PDZ recognizes what?

A

protein substrate 3-4 C-term AAs

213
Q

approximate # genes in c-elegans

A

17000

214
Q

approximate # genes in humans

A

30000

215
Q

jakstate activates gene transcription for ..

A

antiviral response, antitumor response

216
Q

components of transcription complex

A

regulatory sequences, regulatory dna binding proteins, mediator proteins, promoter proximal elements, core promoter, basal transcription complex (RNApol and TFs)

Mol Biochem (6 decks)

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